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2 - Jf rawdataprocess fmt (#725)

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* Fix ROI mapping

* Formatting

* Minor edit

* intial draft of cmake for jungfrau executables Makefile.rawdataprocess

* added the cmake file

* missed Makefile

* added libfmt

* Fix some compiler warnings

* Fix some compiler warnings

* Create filename usining fmt::format

* Rewrite command line parsing with std::string and fmt::format

* Fix file reading

* Fix root string extraction

* Fix ifstream file reading

* Clean up comments

* Add requested changes to helper functions

* fix const&

---------

Co-authored-by: vhinger182 <hinger_v@hv_home_lt1.localdomain>
Co-authored-by: Dhanya Thattil <dhanya.thattil@psi.ch>
This commit is contained in:
hinger_v 2023-05-03 08:43:45 +02:00 committed by GitHub
parent f4e05f7a01
commit 72c992bc74
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GPG Key ID: 4AEE18F83AFDEB23
2 changed files with 148 additions and 144 deletions
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11
slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsData_new.h
View File

@ -406,9 +406,9 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
np = 0; np = 0;
//int pn; //int pn;
// std::cout << dataSize << std::endl; //std::cout << dataSize << std::endl;
if (ff >= 0) //if (ff >= 0) {
// fnum = ff; // fnum = ff; }
if (filebin.is_open()) { if (filebin.is_open()) {
if (filebin.read(data, dataSize)) { if (filebin.read(data, dataSize)) {
@ -417,7 +417,10 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
np = getPacketNumber(data); np = getPacketNumber(data);
return data; return data;
} }
} std::cout << "#";
} else {
std::cout << "File not open" << std::endl;
}
return NULL; return NULL;
}; };

281
slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp
View File

@ -41,12 +41,37 @@
#include <ctime> #include <ctime>
#include <fmt/core.h> #include <fmt/core.h>
std::string getRootString( const std::string& filepath ) {
size_t pos1 = filepath.find_last_of("/");
size_t pos2 = filepath.find_last_of(".");
std::cout << "pos1 " << pos1 << " pos2 " << pos2 << " size " << filepath.length() << std::endl;
return filepath.substr( pos1+1, pos2-pos1-1 );
}
//Create file name string according to slsDetectorPackage format
// dir: directory
// fprefix: fileprefix (without extension)
// fsuffix: filesuffix (for output files, e.g. "ped")
// fext: file extension (e.g. "raw")
// mindex: module index ("d0" in standard)
// findex: file index for one acquisition ("f0")
// aindex: acquisition index (i.e. "run number")
std::string createFileName( const std::string& dir, const std::string& fprefix="run", const std::string& fsuffix="", const std::string& fext="raw", int aindex=0, int mindex=0, int findex=0, int outfilecounter=-1 ) {
std::string filename{};
if (outfilecounter >= 0)
return fmt::format("{:s}/{:s}_d{:d}_f{:d}_{:d}_f{:05d}.{:s}", dir, fprefix, mindex, findex, aindex, outfilecounter, fext);
else if (fsuffix.length()!=0)
return fmt::format("{:s}/{:s}_{:s}.{:s}", dir, fprefix, fsuffix, fext);
else
return fmt::format("{:s}/{:s}_d{:d}_f{:d}_{:d}.{:s}", dir, fprefix, mindex, findex, aindex, fext);
}
int main(int argc, char *argv[]) { int main(int argc, char *argv[]) {
if (argc < 5) { if (argc < 5) {
std::cout std::cout
<< "Usage is " << argv[0] << "Usage is " << argv[0]
<< "indir outdir fname(with formatting, no extension) fextension " << "indir outdir fprefix(excluding slsDetector standard suffixes and extension) fextension "
"[runmin] [runmax] [pedfile (raw or tiff)] [threshold] " "[runmin] [runmax] [pedfile (raw or tiff)] [threshold] "
"[nframes] [xmin xmax ymin ymax] [gainmap]" "[nframes] [xmin xmax ymin ymax] [gainmap]"
<< std::endl; << std::endl;
@ -75,11 +100,11 @@ int main(int argc, char *argv[]) {
int ff, np; int ff, np;
// cout << " data size is " << dsize; // cout << " data size is " << dsize;
ifstream filebin; //ifstream filebin;
char *indir = argv[1]; std::string indir(argv[1]);
char *outdir = argv[2]; std::string outdir(argv[2]);
char *fformat = argv[3]; std::string fprefix(argv[3]);
char *fext = argv[4]; std::string fext(argv[4]);
int runmin = 0; int runmin = 0;
// cout << "argc is " << argc << endl; // cout << "argc is " << argc << endl;
@ -93,9 +118,9 @@ int main(int argc, char *argv[]) {
runmax = atoi(argv[6]); runmax = atoi(argv[6]);
} }
char *pedfile = NULL; std::string pedfilename{};
if (argc >= 8) { if (argc >= 8) {
pedfile = argv[7]; pedfilename = argv[7];
} }
double thr = 0; double thr = 0;
double thr1 = 1; double thr1 = 1;
@ -109,12 +134,7 @@ int main(int argc, char *argv[]) {
if (argc >= 10) { if (argc >= 10) {
nframes = atoi(argv[9]); nframes = atoi(argv[9]);
} }
char ffname[10000];
char fname[10000];
char imgfname[10000];
char cfname[10000];
// Define decoders... // Define decoders...
#if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 && \ #if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 && \
!defined JFSTRXCHIP6 !defined JFSTRXCHIP6
@ -137,36 +157,38 @@ int main(int argc, char *argv[]) {
uint16_t yymax = 0; uint16_t yymax = 0;
#ifndef ALDO #ifndef ALDO
using header = sls::defs::sls_receiver_header; { //THIS SCOPE IS IMPORTANT! (To ensure proper destruction of ifstream)
// check if there is a roi in the header using header = sls::defs::sls_receiver_header;
typedef struct { // check if there is a roi in the header
typedef struct {
uint16_t xmin; uint16_t xmin;
uint16_t xmax; uint16_t xmax;
uint16_t ymin; uint16_t ymin;
uint16_t ymax; uint16_t ymax;
} receiverRoi_compact; } receiverRoi_compact;
receiverRoi_compact croi; receiverRoi_compact croi;
sprintf(ffname, "%s/%s.%s", indir, fformat, fext); std::string fsuffix{};
sprintf(fname, (const char *)ffname, runmin); auto filename = createFileName( indir, fprefix, fsuffix, fext, runmin );
std::cout << "Reading header of file " << fname << " to check for ROI " std::cout << "Reading header of file " << filename << " to check for ROI "
<< std::endl; << std::endl;
filebin.open((const char *)(fname), ios::in | ios::binary); ifstream firstfile(filename, ios::in | ios::binary);
if (filebin.is_open()) { if (firstfile.is_open()) {
header hbuffer; header hbuffer;
std::cout << "sizeof(header) = " << sizeof(header) << std::endl; std::cout << "sizeof(header) = " << sizeof(header) << std::endl;
if (filebin.read((char *)&hbuffer, sizeof(header))) { if (firstfile.read((char *)&hbuffer, sizeof(header))) {
memcpy(&croi, &hbuffer.detHeader.detSpec1, 8); memcpy(&croi, &hbuffer.detHeader.detSpec1, 8);
std::cout << "Read ROI [" << croi.xmin << ", " << croi.xmax << ", " std::cout << "Read ROI [" << croi.xmin << ", " << croi.xmax << ", "
<< croi.ymin << ", " << croi.ymax << "]" << std::endl; << croi.ymin << ", " << croi.ymax << "]" << std::endl;
xxmin = croi.xmin; xxmin = croi.xmin;
xxmax = croi.xmax; xxmax = croi.xmax;
yymin = croi.ymin; yymin = croi.ymin;
yymax = croi.ymax; yymax = croi.ymax;
} else } else
std::cout << "reading error" << std::endl; std::cout << "reading error" << std::endl;
filebin.close(); firstfile.close();
} else } else
std::cout << "Could not open " << fname << " for reading " << std::endl; std::cout << "Could not open " << filename << " for reading " << std::endl;
} //end of protective scope
#endif #endif
jungfrauLGADStrixelsData *decoder = jungfrauLGADStrixelsData *decoder =
@ -213,14 +235,13 @@ int main(int argc, char *argv[]) {
std::time_t end_time; std::time_t end_time;
FILE *of = NULL;
std::cout << "input directory is " << indir << std::endl; std::cout << "input directory is " << indir << std::endl;
std::cout << "output directory is " << outdir << std::endl; std::cout << "output directory is " << outdir << std::endl;
std::cout << "input file is " << fformat << std::endl; std::cout << "input file prefix is " << fprefix << std::endl;
std::cout << "runmin is " << runmin << std::endl; std::cout << "runmin is " << runmin << std::endl;
std::cout << "runmax is " << runmax << std::endl; std::cout << "runmax is " << runmax << std::endl;
if (pedfile) if (pedfilename.length()!=0)
std::cout << "pedestal file is " << pedfile << std::endl; std::cout << "pedestal file is " << pedfilename << std::endl;
if (thr > 0) if (thr > 0)
std::cout << "threshold is " << thr << std::endl; std::cout << "threshold is " << thr << std::endl;
std::cout << "Nframes is " << nframes << std::endl; std::cout << "Nframes is " << nframes << std::endl;
@ -256,8 +277,6 @@ int main(int argc, char *argv[]) {
char *buff; char *buff;
// multiThreadedAnalogDetector *mt=new
// multiThreadedAnalogDetector(filter,nthreads,fifosize);
multiThreadedCountingDetector *mt = multiThreadedCountingDetector *mt =
new multiThreadedCountingDetector(filter, nthreads, fifosize); new multiThreadedCountingDetector(filter, nthreads, fifosize);
mt->setClusterSize(csize, csize); mt->setClusterSize(csize, csize);
@ -285,84 +304,75 @@ int main(int argc, char *argv[]) {
int ifr = 0; int ifr = 0;
char froot[1000]; if (pedfilename.length()!=0) {
double *ped = new double[nx * ny]; //, *ped1;
int pos, pos1; std::string froot = getRootString(pedfilename);
if (pedfile) { std::cout << "PEDESTAL " << std::endl;
if (string(pedfile).find(".dat") != std::string::npos) { if (pedfilename.find(".tif") == std::string::npos) {
pos1 = string(pedfile).rfind("/"); std::string fname = pedfilename;
strcpy(froot, pedfile + pos1); std::cout << fname << std::endl;
pos = string(froot).find(".dat"); std::time(&end_time);
froot[pos] = '\0'; std::cout << "aaa " << std::ctime(&end_time) << std::endl;
}
std::cout << "PEDESTAL " << std::endl; mt->setFrameMode(ePedestal);
// sprintf(imgfname, "%s/pedestals.tiff", outdir);
if (string(pedfile).find(".tif") == std::string::npos) { ifstream pedefile(fname, ios::in | ios::binary);
sprintf(fname, "%s", pedfile); // //open file
std::cout << fname << std::endl; if (pedefile.is_open()) {
std::time(&end_time); std::cout << "bbbb " << std::ctime(&end_time) << std::endl;
std::cout << "aaa" << std::ctime(&end_time) << std::endl;
ff = -1;
while (decoder->readNextFrame(pedefile, ff, np, buff)) {
// if (np == 40) {
if ((ifr + 1) % 100 == 0) {
std::cout
<< " ****"
<< decoder->getValue(buff, 20, 20); // << std::endl;
}
mt->pushData(buff);
mt->nextThread();
mt->popFree(buff);
ifr++;
if (ifr % 100 == 0) {
std::cout << " ****" << ifr << " " << ff << " " << np
<< std::endl;
} // else
//std::cout << ifr << " " << ff << " " << np << std::endl;
if (ifr >= 1000)
break;
ff = -1;
}
pedefile.close();
while (mt->isBusy()) {
;
}
mt->setFrameMode(ePedestal); std::cout << "froot " << froot << std::endl;
// sprintf(fn,fformat,irun); auto imgfname = createFileName( outdir, froot, "ped", "tiff");
filebin.open((const char *)(fname), ios::in | ios::binary); mt->writePedestal(imgfname.c_str());
// //open file imgfname = createFileName( outdir, froot, "rms", "tiff");
if (filebin.is_open()) { mt->writePedestalRMS(imgfname.c_str());
std::cout << "bbbb" << std::ctime(&end_time) << std::endl;
ff = -1; } else
while (decoder->readNextFrame(filebin, ff, np, buff)) { std::cout << "Could not open pedestal file " << fname
// if (np == 40) { << " for reading " << std::endl;
if ((ifr + 1) % 100 == 0) {
std::cout
<< " ****"
<< decoder->getValue(buff, 20, 20); // << endl;
}
mt->pushData(buff);
mt->nextThread();
mt->popFree(buff);
ifr++;
if (ifr % 100 == 0) {
std::cout << " ****" << ifr << " " << ff << " " << np
<< std::endl;
} // else
// cout << ifr << " " << ff << " " << np << endl;
if (ifr >= 1000)
break;
ff = -1;
}
filebin.close();
while (mt->isBusy()) {
;
}
sprintf(imgfname, "%s/%s_ped.tiff", outdir, froot);
mt->writePedestal(imgfname);
sprintf(imgfname, "%s/%s_rms.tiff", outdir, froot);
mt->writePedestalRMS(imgfname);
} else
std::cout << "Could not open pedestal file " << fname
<< " for reading " << std::endl;
} else { } else {
float *pp = ReadFromTiff(pedfile, nny, nnx); std::vector<double> ped(nx * ny);
if (pp && (int)nnx == nx && (int)nny == ny) { float *pp = ReadFromTiff(pedfilename.c_str(), nny, nnx);
for (int i = 0; i < nx * ny; i++) { if (pp && (int)nnx == nx && (int)nny == ny) {
ped[i] = pp[i]; for (int i = 0; i < nx * ny; i++) {
} ped[i] = pp[i];
delete[] pp; }
mt->setPedestal(ped); delete[] pp;
std::cout << "Pedestal set from tiff file " << pedfile mt->setPedestal(ped.data());
<< std::endl; std::cout << "Pedestal set from tiff file " << pedfilename
} else { << std::endl;
std::cout << "Could not open pedestal tiff file " << pedfile } else {
<< " for reading " << std::endl; std::cout << "Could not open pedestal tiff file " << pedfilename
} << " for reading " << std::endl;
}
} }
std::time(&end_time); std::time(&end_time);
std::cout << std::ctime(&end_time) << std::endl; std::cout << std::ctime(&end_time) << std::endl;
@ -373,27 +383,26 @@ int main(int argc, char *argv[]) {
mt->setFrameMode(eFrame); mt->setFrameMode(eFrame);
FILE *of = NULL;
for (int irun = runmin; irun <= runmax; irun++) { for (int irun = runmin; irun <= runmax; irun++) {
std::cout << "DATA "; std::cout << "DATA ";
// sprintf(fn,fformat,irun); std::string fsuffix{};
sprintf(ffname, "%s/%s.%s", indir, fformat, fext); auto fname = createFileName( indir, fprefix, fsuffix, fext, irun );
sprintf(fname, (const char *)ffname, irun); auto imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun );
sprintf(ffname, "%s/%s.tiff", outdir, fformat); auto cfname = createFileName( outdir, fprefix, fsuffix, "clust", irun );
sprintf(imgfname, (const char *)ffname, irun);
sprintf(ffname, "%s/%s.clust", outdir, fformat);
sprintf(cfname, (const char *)ffname, irun);
std::cout << fname << " "; std::cout << fname << " ";
std::cout << imgfname << std::endl; std::cout << imgfname << std::endl;
std::time(&end_time); std::time(&end_time);
std::cout << std::ctime(&end_time) << std::endl; std::cout << std::ctime(&end_time) << std::endl;
// cout << fname << " " << outfname << " " << imgfname << endl; // std::cout << fname << " " << outfname << " " << imgfname << std::endl;
filebin.open((const char *)(fname), ios::in | ios::binary); ifstream filebin(fname, ios::in | ios::binary);
// //open file // //open file
ifile = 0; ifile = 0;
if (filebin.is_open()) { if (filebin.is_open()) {
if (thr <= 0 && cf != 0) { // cluster finder if (thr <= 0 && cf != 0) { // cluster finder
if (of == NULL) { if (of == NULL) {
of = fopen(cfname, "w"); of = fopen(cfname.c_str(), "w");
if (of) { if (of) {
mt->setFilePointer(of); mt->setFilePointer(of);
std::cout << "file pointer set " << std::endl; std::cout << "file pointer set " << std::endl;
@ -414,7 +423,7 @@ int main(int argc, char *argv[]) {
if ((ifr + 1) % 100 == 0) { if ((ifr + 1) % 100 == 0) {
std::cout << " ****" std::cout << " ****"
<< decoder->getValue(buff, 20, 20); // << endl; << decoder->getValue(buff, 20, 20); // << std::endl;
} }
mt->pushData(buff); mt->pushData(buff);
// // //pop // // //pop
@ -426,16 +435,14 @@ int main(int argc, char *argv[]) {
std::cout << " " << ifr << " " << ff << std::endl; std::cout << " " << ifr << " " << ff << std::endl;
if (nframes > 0) { if (nframes > 0) {
if (ifr % nframes == 0) { if (ifr % nframes == 0) {
sprintf(ffname, "%s/%s_f%05d.tiff", outdir, fformat, imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ifile );
ifile); mt->writeImage(imgfname.c_str(), thr1);
sprintf(imgfname, (const char *)ffname, irun);
mt->writeImage(imgfname, thr1);
mt->clearImage(); mt->clearImage();
ifile++; ifile++;
} }
} }
// } else // } else
// cout << ifr << " " << ff << " " << np << endl; //std::cout << ifr << " " << ff << " " << np << std::endl;
ff = -1; ff = -1;
} }
std::cout << "--" << std::endl; std::cout << "--" << std::endl;
@ -444,16 +451,11 @@ int main(int argc, char *argv[]) {
; ;
} }
if (nframes >= 0) { if (nframes >= 0) {
if (nframes > 0) { if (nframes > 0)
sprintf(ffname, "%s/%s_f%05d.tiff", outdir, fformat, ifile); imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ifile );
sprintf(imgfname, (const char *)ffname, irun);
} else {
sprintf(ffname, "%s/%s.tiff", outdir, fformat);
sprintf(imgfname, (const char *)ffname, irun);
}
std::cout << "Writing tiff to " << imgfname << " " << thr1 std::cout << "Writing tiff to " << imgfname << " " << thr1
<< std::endl; << std::endl;
mt->writeImage(imgfname, thr1); mt->writeImage(imgfname.c_str(), thr1);
mt->clearImage(); mt->clearImage();
if (of) { if (of) {
fclose(of); fclose(of);
@ -468,10 +470,9 @@ int main(int argc, char *argv[]) {
<< std::endl; << std::endl;
} }
if (nframes < 0) { if (nframes < 0) {
sprintf(ffname, "%s/%s.tiff", outdir, fformat); auto imgfname = createFileName( outdir, fprefix, "sum", "tiff", -1, 0, 0, -1 );
strcpy(imgfname, ffname);
std::cout << "Writing tiff to " << imgfname << " " << thr1 << std::endl; std::cout << "Writing tiff to " << imgfname << " " << thr1 << std::endl;
mt->writeImage(imgfname, thr1); mt->writeImage(imgfname.c_str(), thr1);
} }
return 0; return 0;